13-81832985-A-G

Variant names:

• chr13-81832985-A-G
• rs261503
• XR_001750061.1:n.79-9763A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001750061.1(LOC105370284):​n.79-9763A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.725 in 151,950 control chromosomes in the GnomAD database, including 40,377 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.73 (40377 hom., cov: 30)
• Consequence: LOC105370284 XR_001750061.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.502
• Publications: 2 publications found

Genes affected

LOC105370284 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.725 AC: 110105 AN: 151832 Hom.: 40354 Cov.: 30

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.795

Gnomad AMR AF: 0.713

Gnomad ASJ AF: 0.753

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.859

Gnomad FIN AF: 0.773

Gnomad MID AF: 0.785

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.743

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.725 AC: 110178 AN: 151950 Hom.: 40377 Cov.: 30 AF XY: 0.730 AC XY: 54208 AN XY: 74270

African (AFR) AF: 0.647 AC: 26786 AN: 41428

American (AMR) AF: 0.713 AC: 10871 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.753 AC: 2613 AN: 3470

East Asian (EAS) AF: 0.994 AC: 5133 AN: 5162

South Asian (SAS) AF: 0.857 AC: 4122 AN: 4808

European-Finnish (FIN) AF: 0.773 AC: 8185 AN: 10582

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.735 AC: 49938 AN: 67948

Other (OTH) AF: 0.746 AC: 1574 AN: 2110

Alfa AF: 0.718 Hom.: 4642

Bravo AF: 0.715

Asia WGS AF: 0.913 AC: 3171 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.9
DANN	Benign	0.66
PhyloP100		-0.50

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs261503; hg19: chr13-82407120;